1. Introduction

MAVEQC is a flexible R-package that provides QC analysis of Saturation Genome Editing (SGE) experimental data. Available under GPL 3.0 from https://github.com/wtsi-hgi/MAVEQC

2. Screen QC

Displays QC plots and statistics for all samples for QC.


2.1. Sample Sheet


2.2. Run Sample QC

2.2.1. Read Length Distrubtion

Displays the percentage of reads for each sample, based on 50 nucleotide increments.


2.2.2. Missing Variants

Missing variants in the library



2.2.3. Total Reads

Displays the total number of reads per sample. Filtering based on 1-dimensional Kmean clustering that excludes unique sequences with low read counts.

  • Accepted reads: Total read count for all unique sequences with sufficient reads.
  • Excluded reads: Total read count for all unique sequences with insufficient reads.


2.2.4. Accepted Reads

Displays the percentage of library reads vs non-library reads (ie. Reference, PAM and Unmapped) for Accepted Reads.

  • Library Reads: Percentage reads mapping to template oligo sequences, including intended variants.
  • Reference Reads: Percentage reads mapping to Reference.
  • PAM_Reads: Percentage reads mapping to PAM/Protospacer Protection Edits (PPEs), without intended variant.
  • Unmapped Reads: Percentage of Unmapped Reads.
  • Library Coverage: Mean read count per template oligo sequence.

Defines the mean read count per template oligo sequence.


2.2.5. Genomic Coverage

Distribution of variants across targeton region based on log2(count+1) values.

Note: missing variants (0 count in the library) are not included.


2.2.6. Genomic Position Percentage

Displays distribution of “LOF” (loss-of-function) vs all “Other” variants across the targeton region, based on read percentages for reference timepoint. Requires concordant distribution of LOF and Other variants.

Note: missing variants (0 count in the library) are not included.


2.3. Run Experiment QC

2.3.1. Sample Correlations



2.3.2. Sample PCA


2.3.3. Fold Change (by category)

condition_D7_vs_D4

condition_D15_vs_D4


2.3.4. Fold Change (by position)

condition_D7_vs_D4

condition_D15_vs_D4


3. QC Results

Summarising the final results, below are the cutoffs using for PASS/FAIL


3.1. Sample QC Results